Magnesium in PDB 4o2b: Tubulin-Colchicine Complex

The structure of Tubulin-Colchicine Complex, PDB code: 4o2b was solved by A.E.Prota, D.Franck, F.Bachmann, K.Bargsten, R.M.Buey, J.Pohlmann, S.Reinelt, H.Lane, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.70 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.310, 157.010, 180.220, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.3

The structure of Tubulin-Colchicine Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Colchicine Complex (pdb code 4o2b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Colchicine Complex, PDB code: 4o2b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Colchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Colchicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.3 occ:1.00 O1B A:GTP501 2.2 20.2 1.0 O A:HOH604 2.2 35.3 1.0 O A:HOH602 2.3 31.6 1.0 O1G A:GTP501 2.4 24.2 1.0 O A:HOH603 2.4 32.3 1.0 PB A:GTP501 3.4 27.6 1.0 PG A:GTP501 3.6 32.5 1.0 OE1 A:GLU71 3.6 53.4 1.0 OD1 A:ASP69 3.8 40.5 1.0 CB A:GLN11 3.9 28.4 1.0 O3B A:GTP501 3.9 52.6 1.0 OD2 A:ASP69 3.9 41.3 1.0 O3A A:GTP501 3.9 40.7 1.0 CG A:GLU71 4.0 45.4 1.0 N A:GLN11 4.1 30.6 1.0 O2G A:GTP501 4.2 34.7 1.0 NZ B:LYS254 4.3 42.6 1.0 CG A:ASP69 4.3 42.1 1.0 CD A:GLU71 4.3 45.6 1.0 OE1 A:GLN11 4.4 36.3 1.0 OD2 A:ASP98 4.5 39.8 1.0 CB A:ASP98 4.5 36.5 1.0 CA A:GLN11 4.5 28.4 1.0 ND2 B:ASN249 4.6 54.7 1.0 O2B A:GTP501 4.7 33.3 1.0 O3G A:GTP501 4.8 25.6 1.0 O1A A:GTP501 4.8 35.4 1.0 PA A:GTP501 4.9 32.1 1.0 CG A:ASP98 4.9 37.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Colchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Colchicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:22.5 occ:1.00 O B:HOH602 2.1 37.5 1.0 OE1 B:GLN11 2.2 32.4 1.0 O C:HOH652 2.2 44.3 1.0 O1A B:GDP501 2.2 28.3 1.0 O B:HOH607 2.4 32.6 1.0 O B:HOH613 2.4 36.5 1.0 CD B:GLN11 3.4 37.1 1.0 O B:HOH690 3.5 65.3 1.0 PA B:GDP501 3.5 27.1 1.0 O B:HOH717 3.7 51.8 1.0 O3A B:GDP501 3.7 37.2 1.0 OD2 B:ASP179 4.0 41.5 1.0 CB B:GLN11 4.0 24.4 1.0 CG B:GLN11 4.2 32.2 1.0 C5' B:GDP501 4.3 28.0 1.0 OD1 B:ASN101 4.4 36.0 1.0 NE2 B:GLN11 4.4 45.0 1.0 O5' B:GDP501 4.4 27.6 1.0 O C:HOH694 4.4 43.4 1.0 OE1 C:GLU254 4.6 56.6 1.0 O2B B:GDP501 4.6 20.3 1.0 O2A B:GDP501 4.6 27.8 1.0 C8 B:GDP501 4.8 28.8 1.0 PB B:GDP501 4.8 27.0 1.0 CG B:ASP179 4.9 41.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Colchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Colchicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:26.9 occ:1.00 O1G C:GTP501 2.0 23.7 1.0 O C:HOH605 2.0 25.6 1.0 O C:HOH613 2.1 28.0 1.0 O1B C:GTP501 2.1 20.8 1.0 O C:HOH818 2.1 24.2 1.0 O C:HOH602 2.2 24.6 1.0 PG C:GTP501 3.2 30.5 1.0 PB C:GTP501 3.2 24.3 1.0 O3B C:GTP501 3.5 41.7 1.0 O3A C:GTP501 3.6 33.3 1.0 O2G C:GTP501 3.8 33.0 1.0 NZ D:LYS254 4.1 29.8 1.0 OD1 C:ASP69 4.1 32.4 1.0 CB C:GLN11 4.1 23.3 1.0 OE1 C:GLU71 4.1 41.2 1.0 OD2 C:ASP98 4.3 41.2 1.0 CG C:GLU71 4.3 38.2 1.0 OD2 C:ASP69 4.3 28.3 1.0 N C:GLN11 4.4 22.1 1.0 O3G C:GTP501 4.4 24.6 1.0 CB C:ASP98 4.5 33.3 1.0 O2B C:GTP501 4.5 27.3 1.0 OE1 C:GLN11 4.5 37.1 1.0 O1A C:GTP501 4.5 26.2 1.0 CG C:ASP69 4.7 32.1 1.0 PA C:GTP501 4.7 24.8 1.0 CD C:GLU71 4.7 41.1 1.0 ND2 D:ASN249 4.8 47.9 1.0 CG C:ASP98 4.9 38.3 1.0 CA C:GLN11 4.9 28.3 1.0 CG D:ASN249 4.9 56.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Colchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Colchicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:54.4 occ:1.00 O D:HOH648 2.2 53.1 1.0 O1A D:GDP501 2.3 60.1 1.0 OE1 D:GLN11 2.6 57.4 1.0 O D:HOH609 2.8 49.8 1.0 OD2 D:ASP179 3.0 82.9 1.0 PA D:GDP501 3.5 54.8 1.0 O3A D:GDP501 3.6 47.7 1.0 CD D:GLN11 3.8 68.6 1.0 OD1 D:ASN101 3.8 69.0 1.0 C5' D:GDP501 4.0 54.3 1.0 O5' D:GDP501 4.2 55.9 1.0 CG D:ASP179 4.2 92.0 1.0 CB D:GLN11 4.5 60.2 1.0 NE2 D:GLN11 4.7 66.9 1.0 O2A D:GDP501 4.7 51.4 1.0 CG D:ASN101 4.7 72.0 1.0 O2B D:GDP501 4.7 42.4 1.0 CG D:GLN11 4.8 64.6 1.0 ND2 D:ASN101 4.8 75.6 1.0 CB D:ASP179 4.8 97.3 1.0 PB D:GDP501 4.9 49.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Colchicine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Colchicine Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:77.7 occ:1.00 O3G F:ACP402 2.3 0.9 1.0 O2B F:ACP402 2.6 84.2 1.0 OD2 F:ASP318 2.8 73.8 1.0 O2A F:ACP402 3.3 0.3 1.0 NH1 F:ARG222 3.5 75.7 1.0 PG F:ACP402 3.5 0.5 1.0 O1G F:ACP402 3.8 0.6 1.0 CG F:ASP318 3.8 67.4 1.0 O5' F:ACP402 3.8 0.3 1.0 PB F:ACP402 3.8 0.7 1.0 C5' F:ACP402 3.9 0.8 1.0 PA F:ACP402 4.0 92.4 1.0 O3A F:ACP402 4.2 0.7 1.0 C3B F:ACP402 4.2 0.9 1.0 OD1 F:ASN333 4.3 94.7 1.0 CD F:GLU331 4.4 87.2 1.0 NH2 F:ARG202 4.5 68.0 1.0 OD1 F:ASP318 4.5 66.1 1.0 OD1 F:ASN242 4.5 0.6 1.0 OE1 F:GLU331 4.6 90.8 1.0 CG F:GLU331 4.6 79.4 1.0 CB F:ASP318 4.6 62.4 1.0 CZ F:ARG222 4.6 79.8 1.0 OE2 F:GLU331 4.7 91.4 1.0 O2G F:ACP402 4.9 0.4 1.0 ND2 F:ASN242 5.0 0.6 1.0

A.E.Prota, F.Danel, F.Bachmann, K.Bargsten, R.M.Buey, J.Pohlmann, S.Reinelt, H.Lane, M.O.Steinmetz. The Novel Microtubule-Destabilizing Drug BAL27862 Binds to the Colchicine Site of Tubulin with Distinct Effects on Microtubule Organization. J.Mol.Biol. V. 426 1848 2014.
ISSN: ISSN 0022-2836
PubMed: 24530796
DOI: 10.1016/J.JMB.2014.02.005